Merge pull request #41 from AU-Biocommons/dev

Terms update and maintenance site

Author: neoformit

app/genomes/management/commands/dump_csv.py

@@ -0,0 +1,33 @@
+"""Dump model data to CSV file."""
+
+import csv
+from django.apps import apps
+from django.core.management.base import BaseCommand
+
+
+class Command(BaseCommand):
+    help = 'Export data from Genome models in CSV format'
+
+    def add_arguments(self, parser):
+        parser.add_argument('model_name', type=str,
+                            help='Name of the model to export')
+        parser.add_argument('-o', '--outfile', type=str,
+                            help='Output file path')
+
+    def handle(self, *args, **kwargs):
+        model_name = kwargs['model_name']
+        Model = apps.get_model('genomes', model_name.capitalize())
+        filename = kwargs.get('outfile', f'{model_name}.csv')
+        field_names = [field.name for field in Model._meta.fields]
+
+        with open(filename, 'w', newline='') as csvfile:
+            writer = csv.writer(csvfile)
+            writer.writerow(field_names)
+            for obj in Model.objects.all():
+                writer.writerow([getattr(obj, field) for field in field_names])
+
+        self.stdout.write(
+            self.style.SUCCESS(
+                f'Data from {model_name} exported successfully to {filename}.'
+            )
+        )

app/home/forms.py

@@ -3,6 +3,7 @@
 import logging
 from captcha.fields import ReCaptchaField
 from django import forms
+from django.utils.safestring import mark_safe
 from .fields import OtherChoiceField
 from . import choices, notify, validators, widgets
 
@@ -26,7 +27,7 @@ class HoneypotSpamFilterMixin(forms.Form):
     # Named to avoid spam bot detection:
     HONEYPOT_FIELD_NAME = 'institution_hp'
     institution_hp = forms.CharField(required=False)
-    honeypot_field = (
+    honeypot_field = mark_safe(
         f'<input type="text" name="{HONEYPOT_FIELD_NAME}"'
         f'  id="id_{HONEYPOT_FIELD_NAME}" required />\n'
         '<script type="text/javascript">\n'

app/home/static/home/css/faq.css

@@ -11,8 +11,14 @@
 }
 #faq-accordion .btn-link:hover {
   color: black;
+  background-color: transparent;
   text-decoration: none;
 }
+#faq-accordion .btn-link:focus {
+  text-decoration: none;
+  outline: none;
+  box-shadow: none;
+}
 #faq-accordion .btn-link::before,
 #faq-accordion .btn-link::after {
   position: absolute;

app/home/templates/home/mail/success_admin_user.html

@@ -34,7 +34,7 @@
         The Principal Investigator is ultimately responsible for the hosted Apollo Instance and must ensure all users adhere to the Apollo Service Terms of Use and Policies;
       </li>
       <li>
-        This Service is designed for the long term storage of genome assembly and annotation data. We can guarantee, that the service will be available to the current operational horizon of the Australian BioCommons (i.e. June 2023)
+        This Service is designed for the long term storage of genome assembly and annotation data. We can guarantee that the service will be available to the current operational horizon of Australian BioCommons (i.e. June 2028)
       </li>
       <li>
         The Service is subject to overall storage quota limits and project administrators and users must monitor their volume of large support files (e.g. BAM) and only host these for the duration they are needed; and

app/home/templates/home/mail/success_admin_user.txt

@@ -4,13 +4,13 @@ You have been nominated by {{ data.name|safe }} as a Project Administrator on th
 
 Once your Instance has been created, you have two options for uploading data to your Apollo Instance. If your data files are greater than 2 GB, we recommend uploading data to your Instance via the command line. To provide you with access to your Instance from the command line, please provide the Apollo Service Team with your public-key. If you are unsure how to generate a public key please see the following help resource.
 
-Alternatively, if your data files are not more than 2 GB, you can upload your files via the Apollo (browser) Interface and you do not need a public-key for this purpose. 
+Alternatively, if your data files are not more than 2 GB, you can upload your files via the Apollo (browser) Interface and you do not need a public-key for this purpose.
 
 Please read and familiarise yourself with the Apollo Service Terms of Use and Policies. Some of the fine print:
 
 The Service is fully subsidised for research groups / consortia where the Principal Investigator is employed by an Australian-based academic or research institute;
 The Principal Investigator is ultimately responsible for the hosted Apollo Instance and must ensure all users adhere to the Apollo Service Terms of Use and Policies;
-This Service is designed for the long term storage of genome assembly and annotation data. We can guarantee, that the service will be available to the current operational horizon of the Australian BioCommons (i.e. June 2023)
+This Service is designed for the long term storage of genome assembly and annotation data. We can guarantee that the service will be available to the current operational horizon of Australian BioCommons (i.e. June 2028)
 The Service is subject to overall storage quota limits and project administrators and users must monitor their volume of large support files (e.g. BAM) and only host these for the duration they are needed; and
 The Apollo Service is not designed for hosting sensitive data.
 You will be notified with login details once your Instance has been created. Additional user resources are located on the Apollo Service website.

app/home/templates/home/resources/faqs.html

@@ -284,7 +284,7 @@ <h5 class="mb-0">
           <a href="/resources/terms"
             >Apollo Service Terms of Use and Policies</a
           >
-          or applicable laws, the Australian BioCommons reserves the right,
+          or applicable laws, Australian BioCommons reserves the right,
           without notice, to restrict or remove access.
         </div>
       </div>
@@ -318,14 +318,8 @@ <h5 class="mb-0">
             >National Collaborative Research Infrastructure Strategy (NCRIS)</a
           >
           investments made by
-          <a href="https://bioplatforms.com/">Bioplatforms Australia (BPA)</a>
-          and the
-          <a href="https://ardc.edu.au/"
-            >Australian Research Data Commons (ARDC)</a
-          >
-          (<a href="https://doi.org/10.47486/PL105"
-            >https://doi.org/10.47486/PL105</a
-          >), investment from the
+          <a href="https://bioplatforms.com/">Bioplatforms Australia (BPA)</a>,
+          investment from the
           <a href=" https://science.des.qld.gov.au/funding/ricf"
             >Queensland Government's Research Infrastructure Co-investment Fund
             (RICF)</a
@@ -657,7 +651,7 @@ <h5 class="mb-0">
           This work is supported by the Apollo Portal Service (<a
             href="/"
             >https://apollo-portal.genome.edu.au</a
-          >) provided by the Australian Biocommons and its partners. The service
+          >) provided by Australian BioCommons and its partners. The service
           receives NCRIS funding through Bioplatforms Australia and the
           Australian Research Data Commons (<a
             href="https://doi.org/10.47486/PL105"

app/home/templates/home/resources/terms.html

@@ -90,7 +90,7 @@ <h3>Apollo Portal</h3>
 
   <h3>Apollo Service</h3>
   <p>
-    The “Apollo Service” (the Service) is offered by the
+    The “Apollo Service” (the Service) is offered by
     <a href="https://www.biocommons.org.au/">
       Australian BioCommons
     </a>
@@ -338,7 +338,7 @@ <h2>
       <strong>Use of service</strong>
       <ol>
         <li>
-          The Apollo Portal and Apollo Service are part of the Australian BioCommons
+          The Apollo Portal and Apollo Service are part of Australian BioCommons'
           suite of services that aim to provide fully subsidised access to publicly
           available services. At the discretion of an Apollo Administrator,
           anonymous use by Anonymous (public) Viewers of data is permitted.
@@ -804,13 +804,12 @@ <h2>
   </h2>
 
   <p>
-    The
     <a href="https://www.biocommons.org.au/">
       Australian BioCommons
     </a>
     (hosted by
     <a href="https://www.unimelb.edu.au/">
-      The University of Melbourne
+      the University of Melbourne
     </a>
     ) operates Apollo Portal Service in collaboration with
     <a href="https://www.qcif.edu.au/">
@@ -820,15 +819,7 @@ <h2>
     <a href="https://science.des.qld.gov.au/funding/ricf">
       Queensland Government's Research Infrastructure Co-investment Fund (RICF)
     </a>
-    , the
-    <a href="https://ardc.edu.au/">
-      Australian Research Data Commons
-    </a>
-    (
-    <a href="https://doi.org/10.47486/PL105">
-      https://doi.org/10.47486/PL105
-    </a>
-    ) and
+    and
     <a href="https://bioplatforms.com/">
       Bioplatforms Australia</a>.
     The Service is underpinned by computational resources provided by the
@@ -2284,9 +2275,9 @@ <h2 id="AusUni">List of Australian Research Institutions</h2>
   </p>
   <p>
     <a id="ref_2"> [2] </a>
-    The Australian BioCommons initiative is hosted by
+    Australian BioCommons is hosted by
     <a href="https://www.unimelb.edu.au/">
-      The University of Melbourne.
+      the University of Melbourne.
     </a>
   </p>
   <p>

app/home/templates/home/signup.html

@@ -250,7 +250,7 @@ <h3>Acknowledgement</h3>
       </p>
 
       <blockquote>
-        This work was supported by the Australian Apollo Service https://apollo-portal.genome.edu.au/ provided by the Australian BioCommons and Operational Partners.
+        This work was supported by the Australian Apollo Service https://apollo-portal.genome.edu.au/ provided by Australian BioCommons and Operational Partners.
       </blockquote>
     </section>
 

app/home/templates/home/snippets/footer.html

@@ -40,7 +40,7 @@
     <section class="footer-bottom-section">
       <div class="copyright">
         The content of this website is licensed under a <a href="https://creativecommons.org/licenses/by/3.0/au/">Creative Commons Attribution 3.0 Australia License.</a>
-        Please review our <a href="/resources/terms">Apollo Service Terms of Use and Policies.</a> The Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia, as well as the Queensland Government RICF
+        Please review our <a href="/resources/terms">Apollo Service Terms of Use and Policies.</a> The Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia, as well as the Queensland Government RICF.
       </div>
     </section>
   </div>

deploy/maintenance-site/apollo-portal.genome.edu.au.conf

@@ -0,0 +1,13 @@
+server {
+    listen 80;
+    server_name  apollo-portal.genome.edu.au apollo-portal-offline.genome.edu.au;
+    access_log   /var/log/nginx/apollo-portal.access.log;
+    error_log    /var/log/nginx/apollo-portal.error.log;
+
+    root /var/www/apollo-portal.genome.edu.au;
+    index index.html;
+
+    location = / {
+        try_files $uri $uri/ /index.html;
+    }
+}